CCR9

C-C motif chemokine receptor 9, the group of CD molecules|C-C motif chemokine receptors

Basic information

Region (hg38): 3:45884425-45903174

Previous symbols: [ "GPR28" ]

Links

ENSG00000173585 ∙ NCBI:10803 ∙ OMIM:604738 ∙ HGNC:1610 ∙ Uniprot:P51686 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCR9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCR9 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	1

Variants in CCR9

This is a list of pathogenic ClinVar variants found in the CCR9 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-45894936-G-T		Hirschsprung disease, susceptibility to, 1	Uncertain significance (Nov 18, 2016)
3-45900828-G-T		Bardet-Biedl syndrome 17	Uncertain significance (Oct 26, 2022)
3-45900834-G-A		not specified	Uncertain significance (Nov 14, 2024)
3-45900862-T-C		not specified	Uncertain significance (Oct 29, 2021)
3-45901038-G-A		not specified	Uncertain significance (Dec 06, 2023)
3-45901046-C-A		not specified	Uncertain significance (Jul 31, 2024)
3-45901074-C-A		not specified	Uncertain significance (Dec 10, 2024)
3-45901130-C-A		not specified	Uncertain significance (Sep 09, 2024)
3-45901194-C-T			Benign (Dec 31, 2019)
3-45901243-T-C		not specified	Uncertain significance (Oct 26, 2024)
3-45901276-T-G		not specified	Uncertain significance (Oct 17, 2023)
3-45901277-G-C		not specified	Uncertain significance (Aug 02, 2022)
3-45901312-T-C		not specified	Uncertain significance (Nov 23, 2024)
3-45901368-G-A		not specified	Uncertain significance (Nov 09, 2022)
3-45901386-A-G		not specified	Uncertain significance (Jul 25, 2024)
3-45901416-C-G		not specified	Uncertain significance (Jun 10, 2024)
3-45901417-T-C		not specified	Uncertain significance (Jan 09, 2024)
3-45901513-T-C		not specified	Uncertain significance (Sep 27, 2021)
3-45901563-G-A		not specified	Uncertain significance (Mar 19, 2024)
3-45901572-G-A		not specified	Uncertain significance (Sep 25, 2023)
3-45901581-T-G		not specified	Uncertain significance (Feb 05, 2024)
3-45901621-C-T		not specified	Uncertain significance (Sep 14, 2022)
3-45901795-G-A		not specified	Uncertain significance (Feb 23, 2023)
3-45901804-G-A		not specified	Uncertain significance (Oct 12, 2021)
3-45901816-G-C		not specified	Uncertain significance (Dec 07, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCR9	protein_coding	protein_coding	ENST00000357632	2	16672

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00420	0.875	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.956	165	203	0.811	0.0000105	2458
Missense in Polyphen		40	57.492	0.69574		755
Synonymous	0.677	73	80.7	0.904	0.00000477	706
Loss of Function	1.31	5	9.32	0.536	3.97e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000601	0.000600
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000791	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.000298	0.000294
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for chemokine SCYA25/TECK. Subsequently transduces a signal by increasing the intracellular calcium ions level. {ECO:0000269|PubMed:10229797, ECO:0000269|PubMed:10640743}.
• Pathway: Chemokine signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Intestinal immune network for IgA production - Homo sapiens (human);Peptide GPCRs;Chemokine signaling pathway;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Chemokine receptors bind chemokines;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.635
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.46

Haploinsufficiency Scores

• pHI: 0.233
• hipred: N
• hipred_score: 0.325

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.412

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ccr9
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; digestive/alimentary phenotype; immune system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: CD8-positive, gamma-delta intraepithelial T cell differentiation;chemotaxis;immune response;cellular defense response;G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;calcium-mediated signaling;cell chemotaxis;chemokine-mediated signaling pathway
• Cellular component: plasma membrane;integral component of plasma membrane;external side of plasma membrane;cell surface
• Molecular function: chemokine receptor activity;C-C chemokine receptor activity;chemokine binding;C-C chemokine binding